HS_code

The code groups in this repository were used in a meta-analysis study of gene expression data related to heat stress in human and mouse (1). Also, this repository is MIT LICENSE.

All code is written in Jupyter Notebook format for easy reproduction.

All figures drawn using these codes can be viewed and downloaded from the figshare collection file (2).

 

1_bar-graph_dataset

How we used these codes (1)

These scripts were used to visualize metadata of gene expression data collected from public databases(Gene Expression Omnibus).

• HS_sample.ipynb

  • Script for visualization of cell types, tissues, and other information in a stacked bar graph.

• HS_treatment.ipynb

  • Script to visualize the exposure time at a certain temperature condition as a bar graph.

• HS_temperature.ipynb

  • Script for visualization of temperature condition information (degree, ℃) in a bar graph.

 

2_scatter-plot_HNscore

How we used these codes (2)

Mainly, we visualized the characteristics of the genes by creating scatter plots with respect to the HN-score (index of analysis: see (1) for details). Note that the code in the Hypoxia_code repository (https://github.com/no85j/hypoxia_code) was used to calculate the HN-score.

1. Visualization of HN-score calculated for all genes

• scatter_plot_HNscore_human.ipynb
• scatter_plot_HNscore_mouse.ipynb

2. Visualization of the distribution of HN-scores of genes shared by human and mouse

• scatter_plot_HNscore_human_vs_mouse.ipynb

3. Visualization integrating HN-score and ChiP-seq data

• scatter_plot_HNscore_ChIP-seq_HSF1.ipynb
• scatter_plot_HNscore_ChIP-seq_HSF2.ipynb
• scatter_plot_HNscore_ChIP-seq_PPARGC1A.ipynb

< Note1 >

ChIP-seq data were obtained using the "Tatget genes" function of the ChIP-Atlas database(3).

 

3_stacked_bar_graph

How we used these codes (3)

These codes were visualized in stacked bar graphs to show which HN-score values of common upregulated and downregulated genes were derived from what samples, sequencing methods, and experimental conditions. The figures created by these codes can be accessed from the figshare file as Figure S2 (URL: https://doi.org/10.6084/m9.figshare.22559752.v4).

• A_sample_type directory
  • HNscore_HN5_sample_type_human.ipynb
  • HNscore_HN5_sample_type_mouse.ipynb
  • stacked_bar_HNscore_sample.ipynb (for visualization)

 

• B_sequencing_method directory
  • HNscore_HN5_sequencing_type_human.ipynb
  • HNscore_HN5_sequencing_type_mouse.ipynb
  • stacked_bar_HNscore_sequencing.ipynb (for visualization)

 

• C_condition directory
  • HNscore_HN5_condition_human.ipynb
  • HNscore_HN5_condition_mouse.ipynb
  • stacked_bar_HNscore_condition.ipynb (for visualization)

< Note2 >

• We are creating a figure by utilizing the human and mouse metadata in Table S1 and 2.

• Table S1 (URL: https://doi.org/10.6084/m9.figshare.22565212.v2)

• Table S2 (URL: https://doi.org/10.6084/m9.figshare.22565311.v4)

 

 

References

1. Yonezawa S, Bono H. Meta-analysis of heat-stressed transcriptomes using the public gene expression database from human and mouse samples. bioRxiv. 2023. p. 2023.04.30.537112. doi:10.1101/2023.04.30.537112

2. Yonezawa S. Meta-analysis of Heat-stressed gene expresssion data in human and mouse. figshare. Collection. 2023. URL: https://doi.org/10.6084/m9.figshare.c.6564487.v2

3. Oki S, Ohta T, Shioi G, Hatanaka H, Ogasawara O, Okuda Y, et al. ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. EMBO Rep. 2018;19. doi:10.15252/embr.201846255